more tests

seroanalytics · Nov 1, 2024 · cd3697c · cd3697c
1 parent 0561a36
commit cd3697c
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Showing 2 changed files with 28 additions and 6 deletions.
diff --git a/tests/testthat/test-convert-log-scale.R b/tests/testthat/test-convert-log-scale.R
@@ -1,29 +1,49 @@
 test_that("Can convert to and from log scale in R", {
   inputs <- data.table::fread(test_path("testdata", "testdata.csv"))
-  log_inputs <- convert_log2_scale(inputs, "me", simplify_limits = FALSE)
-  unlog_inputs <- convert_log2_scale_inverse(log_inputs, "me")
+  log_inputs <- convert_log2_scale(inputs, "me", lower_limit = 2)
+  unlog_inputs <- convert_log2_scale_inverse(log_inputs, "me", lower_limit = 2)
 
   expect_equal(inputs, unlog_inputs)
 })
 
 test_that("Can convert from log scale in R", {
   inputs <- data.table::fread(test_path("testdata", "testdata.csv"))
   res <- convert_log2_scale_inverse(
-    inputs, vars_to_transform = c("me", "lo"))
+    inputs,
+    vars_to_transform = c("me", "lo"),
+    lower_limit = 5)
 
   expect_equal(res$me, 5 * 2^inputs$me)
   expect_equal(res$lo, 5 * 2^inputs$lo)
   expect_equal(res$hi, inputs$hi)
   expect_equal(names(res), names(inputs))
+
+  # try with a different limit
+  res <- convert_log2_scale_inverse(
+    inputs,
+    vars_to_transform = "me",
+    lower_limit = 10)
+
+  expect_equal(res$me, 10 * 2^inputs$me)
 })
 
 test_that("Can convert from log scale in Cpp", {
   inputs <- data.table::fread(test_path("testdata", "testdata.csv"))
   rescpp <- convert_log2_scale_inverse_cpp(
-    inputs, vars_to_transform = c("me", "lo"))
+    inputs,
+    vars_to_transform = c("me", "lo"),
+    lower_limit = 5)
 
   expect_equal(rescpp$me, 5 * 2^(inputs$me))
   expect_equal(rescpp$lo, 5 * 2^(inputs$lo))
   expect_equal(rescpp$hi, inputs$hi)
   expect_equal(names(rescpp), names(inputs))
+
+  # try with a different limit
+  res <- convert_log2_scale_inverse_cpp(
+    inputs,
+    vars_to_transform = "me",
+    lower_limit = 10)
+
+  expect_equal(res$me, 10 * 2^inputs$me)
 })
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -19,7 +19,7 @@ test_that("Can construct stan data", {
   expect_equal(names(stan_data), c("N", "N_events", "id", "value", "censored",
                                    "titre_type", "preds_sd", "K", "N_uncens", "N_lo",
                                    "N_hi", "uncens_idx", "cens_lo_idx",
-                                   "cens_hi_idx", "t", "X", "P", "mu_t0",
+                                   "cens_hi_idx", "t", "X", "P", "upper_limit", "lower_limit", "mu_t0",
                                    "mu_tp", "mu_ts", "mu_m1", "mu_m2", "mu_m3",
                                    "sigma_t0", "sigma_tp", "sigma_ts", "sigma_m1", "sigma_m2",
                                    "sigma_m3"))
@@ -53,7 +53,9 @@ test_that("Natural scale data is converted to log scale for stan", {
   mod <- biokinetics$new(data = dat)
   stan_data <- mod$get_stan_data()
   expect_equal(stan_data$value,
-               convert_log2_scale(dat, "value")$value,
+               convert_log2_scale(dat,
+                                  lower_limit = 5,
+                                  vars_to_transform = "value")$value,
                ignore_attr = TRUE)
 })